Systems and methods for virus detection

Abstract

The present disclosure relates to composition, systems and methods for a wide variety of sample analysis applications, including nucleic acid amplification assays. The system and method includes an integrated, lab-in-a magnetofluidic tube (LIAMT) platform that integrates virus lysis, nucleic acid extraction, isothermal amplification, and CRISPR detection within a single system for molecular detection of viruses.

What is claimed is: 
     
         1 . A device, comprising:
 A reaction vessel comprising a plurality of distinct assay zones comprising a) a lysis zone comprising a lysis/binding buffer and magnetic beads; b) one or more washing zones comprising a washing buffer; c) an amplification zone comprising amplification reagents;   and d) a detection zone comprising nucleic acid detection reagents.   
     
     
         2 . The device of  claim 1 , wherein said assay zones are vertically oriented columns in the reaction vessel. 
     
     
         3 . The device of  claim 2 , wherein the assay zones are separated by a separator. 
     
     
         4 . The device of  claim 1 , wherein the top of the reaction vessel is covered with mineral oil in fluid contact with the top surface of each of the assay zones. 
     
     
         5 . The device of  claim 1 , wherein the amplification zone and the detection zone are in the same assay zone and are separated by wax. 
     
     
         6 . The device of  claim 1 , wherein the device further comprises a blood sample zone comprising a plasma separation membrane. 
     
     
         7 . The device of  claim 1 , wherein the one or more washing zones are three washing zones. 
     
     
         8 . The device of  claim 1 , wherein the amplification reagents are reagents for isothermal amplification of a target nucleic acid. 
     
     
         9 . The device of  claim 8 , wherein the isothermal amplification is recombinase polymerase amplification (RPA) or reverse transcriptase RPA (RT-RPA). 
     
     
         10 . The device of  claim 1 , wherein the nucleic acid detection reagents are reagents for performing a CRISPR assay. 
     
     
         11 . The device of  claim 1 , wherein the reaction chamber is a reaction tube. 
     
     
         12 . The device of  claim 1 , wherein the device is disposable. 
     
     
         13 . A system, comprising a) the device of  claim 1 ; and b) a sample processor comprising a magnetofluidic separation component for magnetofluidic transferring and operation and a incubation/detection component. 
     
     
         14 . The system of  claim 13 , wherein the magnetofluidic separation component and the incubation/detection component comprise a magnetofluidic separation well and an incubation/detection well or a single well configured for magnetofluidic separation and incubation/detection. 
     
     
         15 . The system of  claim 14 , wherein the magnetofluidic well comprises a magnet. 
     
     
         16 . The system of  claim 14 , wherein the incubation/detection well comprises a heater and a thermocouple wire. 
     
     
         17 . The system of  claim 13 , further comprising one or more additional components selected from a microprocessor, a plurality of first stepper motors configured to transfer magnetic beads within assay zones of the device, a plurality of second stepper motors configured to move the device between the magnetofluidic well and the incubation/detection well, and a camera. 
     
     
         18 . A method for detection of a target nucleic acid in a sample, comprising:
 a) contacting the sample with the system of  claim 13 ; and   b) detecting the presence and/or level of the nucleic acid in the sample using the system.   
     
     
         19 . The method of  claim 18 , wherein the nucleic acid is DNA or RNA. 
     
     
         20 . The method of  claim 19 , wherein the nucleic acid is a pathogen nucleic acid selected from SARS-CoV-2 and HIV.